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OpenGene / fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
MIT License
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not detecting adapter seq #93

Open divyoj opened 5 years ago

divyoj commented 5 years ago

Hi!

We are doing riboseq analysis on some fastq files. We are using Fastp for adapter identification and removal. But, we are facing some problems. fastp is able to remove the adapter sequences only if the adapter seq is given in the command line as an argument. It is not able to detect the adapter and remove it by itself and is giving the output as adapter is not detected. The sra file used, adapter seq and codes are as follows:

SRA file : SRR810103 (fastq size 31.6GB)

adapter seq: TCGTATGCCGTCTTCTGCTTG

./fastp -i ./SRR810103.fastq -a TCGTATGCCGTCTTCTGCTTG -q 33 -w 10 -o./output.fastq

./fastp -i ./SRR810103.fastq -w 10 -o ./output.fastq

Can you please help us?

Eagerly waiting for your help!

sfchen commented 5 years ago

I will take a look at the data when time available.

sfchen commented 5 years ago

Could you please try the new version of fastp?

divyoj commented 5 years ago

Thank you for your reply. I tried with the new version also, still not working. Also I tried with other files, its not detecting adaptor in any of them. Though if its given the adaptor seq in command line, its removing it very effectively. i am using fastp --version 0.19.5 I am listing some more files which I tried, SRR1013742 adaptor seq TGTAGGCACCATCAA SRR074359 adaptor seq AAAAAAAAAA